I can never bring myself to side with either the Brotherhood or the Institute because while both have many features I want to like, I can't overlook how blatantly evil both factions are as a whole. If you're like me and believe synths are people, then the Railroad is nobly trying to free an enslaved race.
For example in terms of the Railroad, if you believe synths are not people and are nothing more than the Institute's property, then you could argue that the Railroad is guilty of theft and murder. People's viewpoint on the factions of Fallout 4 comes largely down to their opinion about who and what is considered a person in the Fallout universe.